Using only genome-wide significant SNPs reduces the amount of variance explained by the polygenic score, which is what you describe and I agree with. My comment about the concern about "noise" is with respect to a sibling comment ("Polygenic scores are powerful, but they contain very large amounts of noise compared to the true genetic effects.") That is the "noise" that I was addressing. And just as you say, the noise is, essentially, a worthwhile cost to pay since it should not be directional, and so we use various approaches to include thousands or millions of SNPs in these scores.
> Also, neither of your two problems are the problem here
I don't agree. These problems occur very clearly in any mixed-ancestry analyses, and they have to be carefully accounted for or else they induce between-ancestry bias. It's not a function of the phenotype itself (i.e., I'm not making a comment about intelligence); this is true for all polygenic scores.
Using only genome-wide significant SNPs reduces the amount of variance explained by the polygenic score, which is what you describe and I agree with. My comment about the concern about "noise" is with respect to a sibling comment ("Polygenic scores are powerful, but they contain very large amounts of noise compared to the true genetic effects.") That is the "noise" that I was addressing. And just as you say, the noise is, essentially, a worthwhile cost to pay since it should not be directional, and so we use various approaches to include thousands or millions of SNPs in these scores.
> Also, neither of your two problems are the problem here
I don't agree. These problems occur very clearly in any mixed-ancestry analyses, and they have to be carefully accounted for or else they induce between-ancestry bias. It's not a function of the phenotype itself (i.e., I'm not making a comment about intelligence); this is true for all polygenic scores.